Biology subjects

Clay, D.

Publications and source records attributed to Clay, D..

5 recordsLinked to original sources

bioRxiv2023

BCR-ABL promotes hematopoietic stem and progenitor cell formation in embryonic stem cells

Generating Hematopoietic Stem Cells (HSCs) from Pluripotent Stem Cells (PSCs) has been a long-lasting quest in the field of hematopoiesis. Previous studies suggested that enforced expression of BCR-ABL, the unique oncogenic driver of Chronic Myelogeneous Leukemia (CML), in Embryonic Stem Cells (ESCs)-derived hematopoietic cells is sufficient to confer long-term in vivo repopulating potential. To precisely uncover the molecular events regulated by the Tyrosine-kinase activity of BCR-ABL1 (p210) during the course of hematopoietic differentiation, we engineered a Tet-ON inducible system to modulate its expression in murine ESC. We showed in unique site-directed knock-in ESC model, that BCR-ABL expression tightly regulated by doxycycline (dox) controls the formation and the maintenance of immature hematopoietic progenitors. Interestingly, these progenitors can be expanded in vitro for several passages in the presence of dox. Our analysis of cell surface markers and transcriptome compared to wild-type fetal and adult HSCs unraveled a similar molecular signature. LTC-IC assay confirmed their self-renewal capacities albeit with a differentiation bias towards erythroid and myeloid cells. Collectively, our novel Tet-ON system represents a unique in vitro model to shed lights on ESC-derived hematopoiesis, CML initiation and maintenance. KEY POINTSO_LIWe report a unique BCR-ABL-induced-embryonic stem cell -derived hematopoiesis model in murine embryonic stem cells C_LIO_LIThis BCR-ABL-induced self-renewal and differentiation model can be of major interest to uncover molecular events required for ESC-derived hematopoiesis C_LI

cancer biology↗

bioRxiv2022

Carbon footprint of South Dakota dairy production system and assessment of mitigation options

Livestock production contributes to greenhouse gas (GHG) emissions. However, there is a considerable variability in the carbon footprint associated with livestock production. Site specific estimates of GHG emissions are needed to accurately focus GHG emission reduction efforts. A holistic approach must be taken to assess the full environmental impact of livestock production using appropriate geographical scale. The objective of this study was to determine baseline GHG emissions from dairy production in South Dakota using a life cycle assessment (LCA) approach. A cradle-to-farm gate LCA was used to estimate the GHG emissions to produce 1 kg of energy-and-protein corrected milk (ECM) in South Dakota. The system boundary was divided into feed production, farm management, enteric methane emissions, and manure management as these activities are the main contributors to the overall GHG emissions. The production of 1 kg ECM in South Dakota dairies was estimated to emit 1.21 kg CO2 equivalents. The major contributors were enteric methane emissions (46.3%) and manure management (32.6%). Feed production and farm management made up 13.9 and 7.2 %, respectively. The estimate was similar to the national average but slightly higher than the California dairy system. The source of corn used in the dairies influences the footprint. For example, South Dakota corn had fewer GHG emissions than grain produced in Iowa. Therefore, locally and more sustainably sourced feed input will contribute to further reducing the environmental impacts. Improvements in efficiency of milk production through better genetics, nutrition animal welfare and feed production are expected to further reduce the carbon footprint of South Dakota dairies. Furthermore, use of feed additives and anaerobic digesters will reduce emissions from enteric and manure sources, respectively.

systems biology↗

bioRxiv2021

Spinal cord injury reprograms muscle fibro-adipogenic progenitors to formheterotopic bones within muscles

The cells-of-origin of neurogenic heterotopic ossifications (NHO), which develop frequently in the periarticular muscles following spinal cord injuries (SCI) and traumatic brain injuries, remain unclear because the skeletal muscle harbors two progenitor cell populations: satellite cells (SCs) which are myogenic, and fibro-adipogenic progenitors (FAPs) which are mesenchymal. Lineage-tracing experiments using the Cre recombinase /LoxP system were performed in two mouse strains with the fluorescent protein ZsGreen specifically expressed in either SCs or FAPs in the skeletal muscles under the control of the Pax7 or Prrx1 gene promotors respectively. These experiments demonstrate that following a muscle injury, SCI causes the upregulation of PDGFR on FAPs but not SCs and the failure of SCs to regenerate myofibers in the injured muscle, with instead reduced apoptosis and continued proliferation of muscle resident FAPs enabling their osteogenic differentiation into NHO. No cells expressing ZsGreen under the Prrx1 promoter were detected in the blood after injury suggesting that the cells-of-origin of NHO are locally derived from the injured muscle. We validated these findings in the human pathology using human NHO biopsies. PDGFR+ mesenchymal cells isolated from the muscle surrounding NHO biopsies could develop ectopic human bones when transplanted into immunocompromised mice whereas CD56+ myogenic cells had a much lower potential. Therefore, NHO is a pathology of the injured muscle in which SCI reprograms FAPs to uncontrolled proliferation and differentiation into osteoblasts.

pathology↗

bioRxiv2020

Transcribed germline-limited coding sequences in Oxytricha trifallax

The germline-soma divide is a fundamental distinction in developmental biology, and different genes are expressed in germline and somatic cells throughout metazoan life cycles. Ciliates, a group of microbial eukaryotes, exhibit germline-somatic nuclear dimorphism within a single cell with two different genomes. The ciliate Oxytricha trifallax undergoes massive RNA-guided DNA elimination and genome rearrangement to produce a new somatic macronucleus (MAC) from a copy of the germline micronucleus (MIC). This process eliminates noncoding DNA sequences that interrupt genes and also deletes hundreds of germline-limited open reading frames (ORFs) that are transcribed during genome rearrangement. Here, we update the set of transcribed germline-limited ORFs (TGLOs) in O. trifallax. We show that TGLOs tend to be expressed during nuclear development and then are absent from the somatic MAC. We also demonstrate that exposure to synthetic RNA can reprogram TGLO retention in the somatic MAC and that TGLO retention leads to transcription outside the normal developmental program. These data suggest that TGLOs represent a group of developmentally regulated protein coding sequences whose gene expression is terminated by DNA elimination.

genomics↗

bioRxiv2018

Hierarchical organization of developing HSPC in the human embryonic liver

Despite advances to engineer transplantable hematopoietic stem and progenitor cells (HSPCs) for research and therapy, an in depth characterization of the developing human hematopoietic system is still lacking. The human embryonic liver is at the crossroad of several hematopoietic sites and harbours a complex hematopoietic hierarchy including the first, actively dividing, HSPCs that will further seed the definitive hematopoietic organs. However few is known about the hierarchical phenotypic and functional hematopoietic organization operating at these stages of development.\n\nHere, by using a combination of four endothelial and hematopoietic surface markers i.e. the endothelial-specific marker VE-cadherin, the pan-leukocyte antigen CD45, the hemato-endothelial marker CD34 and the Angiotensin-Converting Enzyme (ACE, CD143), encompassing all early human HSPCs, we identified a hematopoietic hierarchy and, among it, a population co-expressing the four markers that uniquely harbored a proliferation and differentiation potential both ex vivo and in vivo. Moreover, we traced back this population to the yolk sac and AGM sites of hematopoietic emergence. Taken together, our data will help to identify human HSPC self-renewal and amplification mechanisms for future cell therapies.\n\nSUMMARY STATEMENTWe uncover the phenotypic and functional hematopoietic hierarchy operating in the early human embryo. It will bring insights into the mechanisms driving hematopoietic stem cell self-renewal for future cell therapies.

developmental biology↗